The Past and Future Angel
by Fight-of-the-Irish
Summary: Emerging from the 12th angel, Shinji is changed. For better or for worse, only time will tell.
1. Chapter 1

The Difference of an Inch

The Past and Future Angel

Emerging from the 12th angel, Shinji is changed. For better or for worse, only time will tell.

Disclaimer- I do not own Evangelion. If I did, Shinji would not be so annoying.

XxXxX

"Talking"

'Thinking'

XxXxX

Evangelion Units Zero and Two watched helplessly as the ground before them began to shake and sway.

"Is it a reaction to the AT field?!" called out a frantic Misato in the control room.

"Negative" responded Aoba, "they haven't deployed their fields yet!"

Turning her attention back to the screen, she could only watch in a mixture of horror and fascination as the black and white ball of the 12th angel turned solid black before becoming distorted.

From one of the protruding bulges, a crack appeared releasing a stream of red blood down the body and onto the ruined street below. Soon the wound widened and before they knew it a hand clawed its way out of the angel's body.

Not a word was ushered in the command room as the upper torso of Evangelion Unit 1 followed the hand in a groom birth from the angel's corps. Rearing its head it let out a deafening cry.

"My god! Is that what I'm piloting" whispered Asuka as she watched Unit One rip the angel apart and fall down to the ground.

Letting out another defining roar Unit One took a single step forward, the blood streaming down its purple armor making it appear to be a creature of blood.

Unit One took another step and another, all in the direction of the two other Evas.

"Be careful you two!" warned Misato from the control room. "We have no idea of the conditions inside Unit One. It could be going berserk, or it could be controlled by the angel! So watch yourselves!"

Unit One continued it's slow and steady advance and right as the other two Evas were about to take action, something unexpected happened.

Without warning cuts and holes opened up all over Unit One's body and it collapsed in a boneless heap onto the ground.

Before Unit One even hit the ground, Rei was already rushing forward.

'Ikari!' she thought as she pulled the lifeless Eva off the ground.

Reaching to the back where the entry plug is the pulled at the metal shielding the plug. Surprisingly it came of with little effort and as it was flung aside thin strands of blood and flesh could be seen trailing from the mettle back to the body of Unit One.

Reaching in she manually pulled out the entry plug. Her brows came together in a look of concern as she felt the heat coming off of the entry plug. It wasn't enough to damage Unit Zero's hands, but it was hot enough to be uncomfortable, to say the least, for Shinji inside the plug.

Lowering the entry plug to the ground, Rei quickly made her way to the entry plug. In the distance she could see NERV vehicles rushing over the ruined landscape in their direction.

Right as she was about to reach the heated hatch, it was opened from the inside. Reaching her arms out reflexively, she caught Shinji as he fell into her arms in a dead heap. His breathing was raged and blood could be seen coming from his eyes, ears, nose, and mouth.

XxXxX

Shinji was floating.

All around him there was nothing but darkness.

Reaching out his hand he couldn't feel anything and when he looked around all he saw was the same black and empty void.

'How did I get here? The last thing I remember was engaging the Angel. I was sinking into its body.'

Looking around he muttered, "So this is what it's like to be inside an angel?"

Suddenly, without any warning, he felt himself getting pulled by an unseen force. It felt like something was yanking on all of his bones and the flesh was being dragged along with his skeleton.

Letting out a gasp, Shinji closed his eyes to block out the pain.

When he opened his eyes again, he was no longer in an empty void but in a train car.

Outside the city of Tokyo 3 could be seen streaming by the window and the entire landscape was bathed in the orange glow of a setting sun.

Sitting in the seat across from him was a younger version of himself. Strangely this did not concern Shinji in the slightest.

"Who are you?" questioned his younger self.

"I am Ikari Shinji" replied Shinji in slightly confused tone of voice.

"Why?"

"It was the name given to me by my parents, it is what I am known by, people address me as Ikari Shinji!" said Shinji, a since of panic creeping into his voice although he didn't know why the word or his younger self were affecting him so.

"But what do you call yourself?"

"I call my self Ikari Shinji too!"

"Is that what you also call your past self too?"

"Yes, I am Ikari Shinji!"

"But how can that be? The past Ikari Shinji is very different from the present Ikari Shinji. How can you continue to call yourself Ikari Shinji?"

"People change, that's life, but we still remain who we are!" yelled Shinji, the panic evident in his eyes as he put his head in his hands.

Getting up from his seat the younger Shinji walked over to Shinji and put a hand on his shoulder.

Leaning in close, his eyes became covered with his hair and a cruel smile played on his lips, "But you are not Ikari Shinji!"

Opening his eyes, Shinji was greeted with an unfamiliar ceiling and an overhead light. He was covered in sweat and when he tried to sit up he couldn't. Looking down he noticed two things. One, he was completely naked, and two he was strapped to the bed with heavy restraints.

From off to his right he heard a voice, "Ma'am he's regained conciseness."

"This is too soon, sedate him!"

Turning his head he saw a figure in an environmental suite. The glare from the overhead light prevented him from seeing the face and before he could even struggle or ask a question he felt a prick on the side of his neck and the world darkened again.

XxXxX

As Ritsuko can out of the contamination chamber she saw Misato looking into the contamination room through the observation window.

Without even turning to look at her friend, Misato asked, "How bad is it?"

"We don't know yet, I just sent some samples to get tested. On initial checkup the person in there physically seams to be the Shinji we know…"

"But?"

"But there were some small abnormalities that we detected in his bran wave pattern as well as some other things we need to go over. We won't know for sure until the tests get back."

"And what will happen if it is really is Shinji in there?" asked Misato.

"Then he will be released. But the question is… what will you do if that isn't Shinji?"

Misato's face darkened as she looked at the figure on the bed, "Then we will kill it. That room can be sealed off and flooded. That should hold it until we can get one of the Evas to come and crush it."

"That's a hard call to make" said Ritsuko glancing at Misato next to her.

"It's what has to be done to wipe out all the angels."

Turning on her heals Misato left the contamination chamber area. Making her way outside the bunker she looked over at the sight of the pyramid that contains the central headquarters for NERV. Tears began to fall down her face and she made it to her car before completely breaking down.

"Please, please be Shinji!"

XxXxX

Reaching her apartment Misato had cleaned herself up enough that her earlier emotional outbreak was not evident. Unlocking to door she was greeted by Penpen with his food dish.

Smiling she said, "Ok, lets get you something to eat."

Going to the fridge she pulled out some fish and put it in the dish. While she was doing this she called out to the seemingly empty apartment.

"Asuka, you here?"

"Yea I'm here" replied the redhead as she stuck her head outside of her room. "Any word about the idiot?"

"No, nothing yet. Ritsuko is still running tests to verify that it is Shinji and not the angel" said Misato as she sat down at the table with a beer.

"It's that idiot's fault for rushing in like that" said Asuka sitting down at the table.

"Asuka, let's not start this again! I'll chew him out when he get back..."

Asuka was silent, but thought, 'That's if he get's back.'

XxXxX

That night in her office, Ritsuko was going over the results of the tests done on Shinji.

DNA and brainwave analysis came back that it was Shinji, but there were changes in the spectrum of his brain waves. It was almost like…

Before she could ponder this new development any further, the door to her office opened up. Turning around she was greeted with the sight of Commander Ikari walking through the door.

Giving him a smile she turned back to her screen. When the commander was standing right behind her she began to speak.

"The test results came back. That person physically is Shinji. No abnormalities were detected in his body or his DNA. But what concerns me is his brain waves" she said as she brought up the screen on her computer.

"Here are Shinji's brain waves before the battle and these," she said bringing up another graph over the old one, "are his brain waves now."

Looking at the graphs you could see that they lined up perfectly with each other, showing that they are from the same person. But the color of the two was different, showing a difference in the frequency that the brain waves were running at.

"Originally his waves were red like a normal human, but now they are a purple, almost blue pattern. It's like he is now part angel or is turning into one. The only place I've ever seen this is with Rei."

The commander was silent for a few minutes as he looked over the data and ran the scenario in his mind.

"This will not be a problem" he said in a cold voice.

"But sir, what will happen if this growth continues? He could turn into a full fledged angel right under our noses."

"Not if we control him properly. And besides even if he becomes a fully realized angel there is still a high probability that he will be under our control. This will not affect the scenario at all."

Looking at the commander Ritsuko suppressed a shudder at the coldness of the man. It was this same coldness and cunning that she found so attracting in her superior officer.

"How do you suggest we control him? He is given considerable freedoms when he's not at NERV, from living with Misato to going to school."

The commander was silent at this for a moment before a smile appeared on his face. "We will hold him in the contamination chamber for the next two weeks before releasing him back to Misato. And we'll tell her exactly what has happened to Shinji. Her hate of the angels will make her keep a closer eye on the boy and this knowledge will help to separate him from his friends at school and the second child."

"What about Rei? She has always been close to him and this might just increase it?"

"Such situation is unavoidable. Besides, it is only a matter of time before the third Rei is awakened. So as long as she is still loyal to me, her relations with my son are of no concern."

XxXxX

Shinji slowly opened his eyes. The same unfamiliar ceiling and the bright light greeted him.

'Great, I was hoping that was just a dream'

Looking down at his body he saw that he had been put in a hospital dress, but was still strapped down to the table.

Looking to his right and left he saw that no one was in the room, but there were cameras, one on each wall.

After laying there for a few minutes the crackle of an intercom filled the room and was soon followed my Ritsuko's voice.

"Shinji, you are in the contamination chamber… Do you remember what happened with the Angel?"

Pausing for a moment, Shinji thought back, "I remember being sent out against the angel and then being sucked into the angel. After that my memory becomes hazy. I think I had a dream were I was floating in the dark before talking to a younger version of myself on a train."

In the monitoring room Ritsuko's eyebrows went up at this comment and she wrote down, 'Possible contact with the angel'

"What did you talk about with your younger self?"

"He kept on saying that I am not me. I tried to say that I am me but he kept on saying that I wasn't. For some reason this really bothered me."

Hearing this Ritsuko wrote down, 'Possibility that Angel or his subconscious told him that he is no longer human.'

"Why are you asking about that, I thought it was just a dream?"

Ritsuko paused before answering. The commander never told her not to tell him about what happened, and it would defiantly server to control him more if he knew he could never run away.

"There is a possibility that you weren't dreaming. In all likelihood, that was either the angel or your subconscious talking to you. The truth is that that you've been contaminated by the angel."

XxXxX

That's it from the first chapter, I hope you enjoyed it. I will be following the anime for the angels that appear but I will be going with the manga for the character's personalities.

Please tell me what you think!

Ja Ne!


	2. Chapter 2

The Past and Future Angel

Disclaimer- I do not own Evangelion. If I did, Shinji would not be so annoying.

XxXxX

"Talking"

'Thinking'

XxXxX

"Contaminated by the angel"

These words echoed through out Shinji's head as he lay there, strapped to the examination table.

"What's going to happen to me now?" he remembered asking Ritsuko when she told him the news.

There was a pause before the doctor responded.

"You will be kept here in the contamination chamber while we run some test to determine just what happened to you. After that if everything checks out, them you can go home."

"But what happens if an angel attacks, or everything doesn't check out fine?" asked Shinji with a hint of panic in his voice.

"If an angel attacks then Asuka and Rei will take care of it. Already Evangelion Unit Four is being shipped from the Massachusetts NERV facility and the fourth child is being selected. As for what will happen if you don't check out ok…it's best not to think of that" responded Ritsuko with the sound of some guilt penetrating her voice.

These words were replayed is Shinji's head over and over again, each time thinking about just what the worst case scenario was. And each time, the worse case scenario resulted in even more dreadful consequences for him until he finally fell asleep with the thought of Unit One's hand coming down to crush him.

When Shinji woke up, nothing had changed.

The room was still brightly lit, and he was still strapped to the bed in a hospital gown.

He lay there, staring up at the ceiling and thinking for what seemed to be a couple of hours when he heard the sound of the door opening.

Turning his head as much as he could he saw a person dressed in a red environmental suit entering the room.

Judging by the figure in the tight body suit, Shinji accurately assumed that the person was a female. Unfortunately the glare of the lights reflected off the helmet make it impossible to see her face.

"Good morning Shinji" came Dr. Akagi's voice from the figure.

"Morning" replied Shinji as Dr. Akagi came closer. "Any possibility that I'll be getting out soon?"

"No, no, I'm afraid not" she said as she brought a table full of medical devices next to his bed.

Reaching over and grabbing a needle she began to prep Shinji to take a blood sample. "We still need to perform many tests to determine the exact nature of your contamination and to see if it's harmful to yourself or those around you."

Shinji just laid there is silence as Ritsuko continued to poke and prod his as she took samples of his blood, bloody temperature, and other bodily statistics.

Suddenly the door opened again and in entered another person in an environmental suit, this time a man. Be was pulling in a machine that vaguely resembled the machine that eye doctors use to check your eyes, but this one has a large power cable attached to a black box at it's base.

"Almost done Shinji" said Ritsuko from her position next to him as she and the man began to set up the machine. "I just need to take a scan of your body and we will be done for today."

As the man continued to set up the machine, Ritsuko was making some last minute adjustments to Shinji himself.

"So Shinji" she said conversationally, "Have you ever seen one of these before?" she asked motioning to the machine.

"No, I haven't. What is it? You said it would scan my body but it's not anything I've seen before?"

"It's a new mutli-scanner. It takes x-rays, MRIs, and other body scans" Ritsuko responded in a happy voice, like a kid showing off one of her favorite toys. "Each lenses take a different scan and with it the long and tedious process of taking the individual scans is removes. Also the size has been greatly reduced for ease of transportability."

"It's still brand new and there are only 6 in all of Japan, and NERV owns two of them" came the voice of the man working on the machine. "Dr. Akagi, could you please steep back so I can take the scan."

As soon as she steeped back the machine began to hum and click as the man moved it up and down Shinji's body multiple times. After a minute or two, the scanning was done and the machine was silent once again.

"That's it for today, Shinji. I'll let you know the results of the test latter, but for now, I think it's best if you rest" said Ritsuko as she put a pill in Shinji's mouth.

Swallowing the pill with out complaint, Shinji became very tired as was soon asleep.

XxXxX

Later that night, Ritsuko began to study the results of the scans done as it was being displayed across multiple computer monitors.

While still human, her earlier observations of how Shinji was like Rei, a half angel, were conformed.

Already his body's chemical composition was changing slightly as well as his brain wave level.

Chuckling to herself Ritsuko brought up a screen showing Rei's readouts and compared them to Shinji. The two had always been close to each other before, but not they were almost identical.

"So this is how the scenario will turn out" came a voice from behind her.

Whirling around in her chair, Ritsuko came face to face with the commander. She was so absorbed in the data that she didn't even hear the door open or him walk in.

"The earlier observations have been conformed" reported Ritsuko, "Shinji is in the beginning stages of turning into an angel."

"Do we have any idea of the form he will take?"

"At this moment, no. But given that his body has remained almost unchanged, I will say that he will continue to reside in his current form or something very similar."

The commander was silent for a moment before asking, "And what of his ability to pilot Unit One?"

Ritsuko was slightly taken back by this. Wasn't the man at all concerned that his son was turning into an angel before his very eyes?

"He should still be able to pilot. In fact, his sync ration will probably be even better. The question is how will Unit One react to him?"

Thinking this information over Gendo came to his conclusion, "We will continue with the previous plan. Everyone, including the Third Child, will know that he's been contaminated. The truth that he's become an angel will remain out secret."

Silence permeated the room as the two continued to look over the data.

"So commander," Ritsuko tried to say conversationally, "why are you here so late?"

"I was with Rei working on the Dumb Plug system."

"Oh" said Ritsuko the conversation effectively over.

Elsewhere in the Geofrount Rei was walking through the silent halls.

The late night rendezvous with the commander occurred as normal, with Rei floating in a tank of LCL naked while scans were taken and the commander watched.

If she got early like tonight she would return to her apartment and try to get some sleep before the new day stated. However the work on the Dummy Plug system usually took all night, forcing her to miss school the next day.

But tonight the commander seemed distracted. While she didn't ask him what was bothering him but she had and idea, for the same thing was on her mind. Since his rescued, she had not been able to see Shinji. She knew he was contaminated by the 12th angel and was being held in the contamination facility, but she didn't know his actual condition.

Making her way to the contamination chamber Rei stopped in front of the viewing window. Inside the room the lights were on and Shinji was laying on the bed in the center of the room.

Rei noticed the straps holding him down as well as the rhythmic breathing that was coming from his sleeping form.

'He seams healthy' thought Rei looking at Shinji.

She expected to see the straps holding him down due to the procedures when dealing with a pilot who has had contact with an angel and trusted the commander when he said that Shinji was fine, but to actually see him somehow eased her mind.

She continued to stand watching him for a little bit, noticing that if wasn't for the straps he would be tossing and turning in the bead, his eyes rapidly moving under his eyelids.

XxXxX.

In Shinji's dream he was walking around Tokyo 3 in his normal school uniform.

The city was devastated with roads torn up, buildings collapsed, and massive craters filled with red water everywhere.

Wherever he looked a sense of despair permeated the silent streets and when the wind blew it sounded like a person wailing.

But what really began to get to Shinji was the absolute lack of any sings of life.

Wherever he looked there were no people or any animals. It was as if what ever great catastrophic event that happened here took all life with it.

"What has happened here?" he muttered to himself as he continued to wander to lifeless city.

Reaching an extremely large crater filled with the same red colored liquid he sat down on one of the pieces of a building that were littering the edge of the crater.

Looking out at the lake Shinji repeated his question, 'What the hell is going on?'

Suddenly off to his right a loud splash filled the air and ripples began to spread across the water. Looking over in that direction, all that was there was a broken lamp post with the light sticking out of the water where the ripples were coming from.

Off to his left Shinji thought he heard the fluttering of wings but when he looked in that direction there was nothing there.

"Life is lived but once" came a voice from behind Shinji.

Jumping slightly Shinji turned around to see…nothing.

"We are but candles in the dark" came the disembodied voice from his left.

"Shining brightly in the dark before burning out" the voice came from above.

"Destined only to have our afterimage linger in the dark" the voice came from the right.

"Before being outshined by even brighter lights" the voice came from in front.

During the speech, Shinji was looking around franticly. He tried to see where the voice was coming from but saw nothing.

"Who are you?" asked the voice.

"W-what!" exclaimed Shinji startled, not expecting the sudden question.

"Who are you?" the voice asking again, the surrounding landscape disappearing leaving Shinji standing on a piece of building in the middle of a sea of red liquid.

"I am Ikari Shinji!" yelled Shinji from his spot.

"No" came a sudden booming voice that seemed t come from everywhere at once.

"Who are you?" resumed the questioning voice, this time from Shinji's right.

Turning that direction there was nothing there, but when he looked down at the water, instead of seeing his reflection he was meet with the appearance of his younger self.

Startled, Shinji stepped back, causing him to fall into the sea of red liquid. As he fell into the liquid the block he was standing on disappeared, leaving Shinji alone in the middle of a sea of…blood?

Shinji began to desperately try to stay afloat only to fail while during his struggle he heard the disembodied voice above his ask yet again, "Who are you?"

Shinji began to sink below the surface and was starting to drown when he felt someone grab hold of him.

Opening his eyes his vision was clouded by the blood but through it he saw a glowing female angel pulling him out of the blood. As Shinji's vision began to clear the angel was replaced by the vision of Rei standing over him with a look of concern across her face.

Shinji was still tied to the bed, but was completely drenched in sweat with his hair tightly clinging to his forehead.

"A-Ayanami?" Shinji questioned as he look.

"Are you all right Ikari?"

Shinji dumbly nodded his head as he looked up at Rei.

"What are you doing in here?" questioned Shinji as he glanced towards the door.

"I was in NERV tonight and decided to visit you. It seemed like you were suffering so I came in to wake you up" Rei said in a monotone voice.

This statement took Shinji back.

"But" Shinji said confused, "I'm in the contamination chamber! You can't just come in here with out an environmental suit on!"

"You needed help" said Rei, still standing over Shinji.

"But it's not safe for you to be in here!"

"Why do you say that?" questioned Rei.

"Well…" Shinji said thinking about it, "because I'm in the contamination chamber, so there must be something wrong with me."

"It is ok Ikari. There is no risk of you contaminating me."

"What?"

"Like I said before, there is no risk of me being contaminated by you due to your contact with the angel."

Confused Shinji asked, "Then why am I in here?"

"It is unclear of how you will react to being touched by the angel, so this is merely a precaution" said Rei in a somewhat caring voice.

"But-" Shinji started to say but was stopped by Rei putting her hand on his forehead and gently pushing his head back onto his pillow.

"Ikari, you need to rest now. I will come back and visit latter."

"Ok" mumbled Shinji, a blush forming on his cheeks as Rei held her hand against his forehead and he guiltily enjoyed the feeling of her smooth skin against his.

But the moment couldn't last forever as Rei removed her hand and left the room.

Just as she was leaving she looked over her shoulder, "Goodnight Ikari."

"Goodnight Ayanami."

XxXxX

The next day instead of going to school, Rei was called into the NERV headquarters by the commander.

Entering his office and approaching his desk Rei saw that there were pictures scattered across the surface of the desk. As she got closer she saw that they were pictures of her from the night before.

They showed her standing outside of the contamination chamber, entering it, talking with Shinji, and exiting the contamination chamber.

"Explain yourself pilot" ordered the commander in a harsh voice.

"I went to see how he was doing. He appeared distressed so I aided him and after I explained why I was there I left" reported Rei as soon as the commander ordered her to.

"You broke containment protocols. What would you have done if he was a threat or carrying a pathogen from the angel?"

"That would not be a problem for me sir."

"You are overstepping you boundaries. You will follow all contamination protocols when dealing with an Angel or else. Am I clear?"

Rei knew what the commander was implying. She was disposable and another one could easily be awakened to replace her. "I understand sir."

"Good, I'm ordering you to stay away from the contamination chamber until further notice" said the commander as he adjusted his glasses.

Rei knew this might happen but was still taken aback by it. Thinking about the order she carefully chose her words, "I will have to decline following those orders sir."

"Oh really" said the commander, his eyebrow raising in an arch. "Explain!"

"I have already promised pilot Ikari that I would visit him. Also I feel that I will be able to help him come to terms with what has happened to him."

"And how can you do that?" questioned the commander, not liking were this was going.

"I know that the contact with the angel has changed pilot Ikari into something different… something similar to what I am."

"How do you know this?" demanded Gendo as he was beginning to get nervous.

"It is something I felt when I was around him. I first had a suspicion when he emerged from the 12th angel but I feel that I was right when I made contact with him last night" stated Rei as she looked at the commander.

Gendo almost let out a sigh. He had wanted to keep the truth about Shinji's condition a secret until the boy was no longer needed, but now he might as well tell Rei.

"Your suspicions are correct. The contamination from the prolonged exposure with the 12th angel has set Shinji on the road to becoming an angel. Already his is part angel, similar to yourself. But instead of being fused with part of Lilith, he is merged with part of the 12th angel."

"And what will become of him?" softly questioned Rei, feeling concerned for her fellow pilot.

"So far besides us in this room, only Dr Akagi and the subcommand know the truth of the Third Child's condition. We intend to keep it that way. He will be used to further the scenario and act as our personal backup card in case SEELE tries anything in the end. All that everyone else will know will be that he was contaminated by the angel, and that's it."

"Will you tell Pilot Ikari what happened to him?" asked Rei.

The commander did not answer this question. Either he didn't want to give her an answer or he was still considering his options.

"You may leave Rei…and I will allow you to see the Third Child. Make sure he doesn't loose control" said the commander as he dismissed Rei with nod.

Once Rei left the room, the subcommand stepped out of the shadows off the corner of the office and approached Gendo.

"She is becoming troublesome" said Gendo with out looking at the subcommand as he approached the desk.

"She is a teenage girl."

"That is irrelevant, just as long as she is loyal to me."

"We have starved her of almost all social contact her entire life except for us, so why is she now becoming suddenly…independent?" Gendo mused, more to himself than to the subcommand.

Silence permeated the room as the two men silently thought it over.

"It might be because it's Shinji" said the subcommand thoughtfully.

"Explain what you mean" said Gendo turning towards Fuyutsuki.

"She has always been close to Shinji, mostly due to him reaching out to try to communicate with her on a peer level, something that never happened to her before" said Fuyutsuki. "And now that initial bond they formed through friendship is increasing due to Shinji's…condition."

At this statement Gendo raised an eyebrow and Fuyutsuki continued, "What I mean is that Shinji is now closer to her physically and genetically speaking than anyone else. A familiar presence or, if you want to look at it, a fellow half angel."

Fuyutsuki's lips raised a little and his next words put a frown on Gendo's face, "She could also just like him too."

XxXxX

So what did you think? This was one of those chapters that took a life of it's own while writing, so I home you like it.

Please tell me what you think!


End file.
